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Article: In-depth cDNA Library Sequencing Provides Quantitative Gene Expression Profiling in Cancer Biomarker Discovery

TitleIn-depth cDNA Library Sequencing Provides Quantitative Gene Expression Profiling in Cancer Biomarker Discovery
Authors
Keywordsbiomarker
cDNA sequencing
expressed sequence tag
mutation detection
sequence-specific subtraction
sequencing depth
Issue Date2009
PublisherKexue Chubanshe.
Citation
Genomics, Proteomics And Bioinformatics, 2009, v. 7 n. 1-2, p. 1-12 How to Cite?
AbstractQuantitative gene expression analysis plays an important role in identifying differentially expressed genes in various pathological states, gene expression regulation and co-regulation, shedding light on gene functions. Although microarray is widely used as a powerful tool in this regard, it is suboptimal quantitatively and unable to detect unknown gene variants. Here we demonstrated effective detection of differential expression and co-regulation of certain genes by expressed sequence tag analysis using a selected subset of cDNA libraries. We discussed the issues of sequencing depth and library preparation, and propose that increased sequencing depth and improved preparation procedures may allow detection of many expression features for less abundant gene variants. With the reduction of sequencing cost and the emerging of new generation sequencing technology, in-depth sequencing of cDNA pools or libraries may represent a better and powerful tool in gene expression profiling and cancer biomarker detection. We also propose using sequence-specific subtraction to remove hundreds of the most abundant housekeeping genes to increase sequencing depth without affecting relative expression ratio of other genes, as transcripts from as few as 300 most abundantly expressed genes constitute about 20% of the total transcriptome. In-depth sequencing also represents a unique advantage of detecting unknown forms of transcripts, such as alternative splicing variants, fusion genes, and regulatory RNAs, as well as detecting mutations and polymorphisms that may play important roles in disease pathogenesis. © 2009 Beijing Genomics Institute.
Persistent Identifierhttp://hdl.handle.net/10722/79853
ISSN
2015 SCImago Journal Rankings: 1.058
References

 

DC FieldValueLanguage
dc.contributor.authorYang, Wen_HK
dc.contributor.authorYing, Den_HK
dc.contributor.authorLau, YLen_HK
dc.date.accessioned2010-09-06T07:59:29Z-
dc.date.available2010-09-06T07:59:29Z-
dc.date.issued2009en_HK
dc.identifier.citationGenomics, Proteomics And Bioinformatics, 2009, v. 7 n. 1-2, p. 1-12en_HK
dc.identifier.issn1672-0229en_HK
dc.identifier.urihttp://hdl.handle.net/10722/79853-
dc.description.abstractQuantitative gene expression analysis plays an important role in identifying differentially expressed genes in various pathological states, gene expression regulation and co-regulation, shedding light on gene functions. Although microarray is widely used as a powerful tool in this regard, it is suboptimal quantitatively and unable to detect unknown gene variants. Here we demonstrated effective detection of differential expression and co-regulation of certain genes by expressed sequence tag analysis using a selected subset of cDNA libraries. We discussed the issues of sequencing depth and library preparation, and propose that increased sequencing depth and improved preparation procedures may allow detection of many expression features for less abundant gene variants. With the reduction of sequencing cost and the emerging of new generation sequencing technology, in-depth sequencing of cDNA pools or libraries may represent a better and powerful tool in gene expression profiling and cancer biomarker detection. We also propose using sequence-specific subtraction to remove hundreds of the most abundant housekeeping genes to increase sequencing depth without affecting relative expression ratio of other genes, as transcripts from as few as 300 most abundantly expressed genes constitute about 20% of the total transcriptome. In-depth sequencing also represents a unique advantage of detecting unknown forms of transcripts, such as alternative splicing variants, fusion genes, and regulatory RNAs, as well as detecting mutations and polymorphisms that may play important roles in disease pathogenesis. © 2009 Beijing Genomics Institute.en_HK
dc.languageengen_HK
dc.publisherKexue Chubanshe.en_HK
dc.relation.ispartofGenomics, Proteomics and Bioinformaticsen_HK
dc.subjectbiomarkeren_HK
dc.subjectcDNA sequencingen_HK
dc.subjectexpressed sequence tagen_HK
dc.subjectmutation detectionen_HK
dc.subjectsequence-specific subtractionen_HK
dc.subjectsequencing depthen_HK
dc.titleIn-depth cDNA Library Sequencing Provides Quantitative Gene Expression Profiling in Cancer Biomarker Discoveryen_HK
dc.typeArticleen_HK
dc.identifier.openurlhttp://library.hku.hk:4550/resserv?sid=HKU:IR&issn=1672-0229&volume=7&spage=1&epage=12&date=2009&atitle=In-depth+cDNA+Library+Sequencing+Provides+Quantitative+Gene+Expression+Profiling+in+Cancer+Biomarker+Discoveryen_HK
dc.identifier.emailYang, W:yangwl@hkucc.hku.hken_HK
dc.identifier.emailLau, YL:lauylung@hkucc.hku.hken_HK
dc.identifier.authorityYang, W=rp00524en_HK
dc.identifier.authorityLau, YL=rp00361en_HK
dc.description.naturelink_to_OA_fulltext-
dc.identifier.doi10.1016/S1672-0229(08)60028-5en_HK
dc.identifier.pmid19591787-
dc.identifier.scopuseid_2-s2.0-67649649762en_HK
dc.identifier.hkuros160938en_HK
dc.relation.referenceshttp://www.scopus.com/mlt/select.url?eid=2-s2.0-67649649762&selection=ref&src=s&origin=recordpageen_HK
dc.identifier.volume7en_HK
dc.identifier.issue1-2en_HK
dc.identifier.spage1en_HK
dc.identifier.epage12en_HK
dc.publisher.placeChinaen_HK
dc.identifier.scopusauthoridYang, W=23101349500en_HK
dc.identifier.scopusauthoridYing, D=35197469900en_HK
dc.identifier.scopusauthoridLau, YL=7201403380en_HK

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